I've set up PDT/Xdebug to debug a php application on a remote server.
To accomplish this, I basically start with a copy of the app on my local
machine and then upload that app to the remote machine with RSE/SSH.
When I make edits to the copies on the local machine I synchronize the
app on the remote machine with the app on my local machine. This works
well.

Here's the problem:
The application on the remote server modifies the contents within its
directory tree, so my local app is out of sync with my remote app, but
my local app is the one that should be updated.

Is there any way of getting RSE, to sync from the server to the client
on demand?